bowtie | An ultrafast memory-efficient short read aligner | Genomics library

In Snakemake, conda environments can be easily set up by defining rules as such conda: "envs/my_environment.yaml". This way, YAML files specify which packages to install prior to running the pipeline.

Some software requires a path to third-party-software, to execute specific commands.

An example of this is when generating a reference index with RSEM (example from GitHub page DeweyLab - RSEM):

I have a list ('dummy"). I want to extract ONLY the values related to the best 'Score'. For example, from the list I should have the following values extracted:

This question is related to this other one: How can I read data from a list and index specific values into Elasticsearch, using python?

I have written a script to read a list ("dummy") and index it into Elasticsearch. I converted the list into a list of dictionaries and used the "Bulk" API to index it into Elasticsearch. The script used to work (check the attached link to the related question). But it is no longer working after adding "timestamp" and the function "initialize_elasticsearch".

So, what is wrong? Should I be using JSON instead of the list of dictionaries?

I have also tried using only 1 dictionary of the list. In that case there is no error but nothing gets indexed.

THIS IS THE ERROR

THIS IS THE LIST (dummy)

I have a list (see LIST) that I want to send to a dictionary.

But I do not want to send all the data. Just some values (see SOME VALUES/FEATURES) which happen to repeat many times. For example, the word "Model: xxx" appears like 7 times. "xxx" is the name of the model and it will change.

So far I can only put in the dictionary the last values of the list. How can I put all the values from the list into the dictionary?

SOME VALUES:

Labels: xxxx

Model: xxxx

Image: xxxx

Inference: xxxx

Score: xxxx

TPU_temp(°C): xxxx

Time(ms): xxx ---There are 2 of these, I do not know if it is possible to extract ONLY the second one. But if not, no problem. Extracting both will be fine.--

THIS IS THE CODE - ATTEMPT 1

I have used "paramiko" to connect from my PC to a devboard, and execute a script. Then I am saving the results of this script in a list (output). I want to extract some values of the list and insert them into Elasticsearch. I have done it manually with the first result of the list. But how can I automate for the rest of the values? Do I need "regex"? Please give me some clues.

Thank you

THIS IS PART OF THE CODE THAT CONNECTS TO THE DEVBOARD, EXECUTES A SCRIPT AND RETRIEVES A LIST=output

Hi I'm stuck trying to solve this: class Classy, to represent how classy someone or something is. "Classy". If you add fancy-looking items, "classiness" increases!

Create a method, addItem() in Classy that takes a string as input, adds it to the "items" array and updates the classiness total.

Add another method, getClassiness() that returns the "classiness" value based on the items.

The following items have classiness points associated with them:

1. "tophat" = 2
2. "bowtie" = 4
3. "monocle" = 5

Everything else has 0 points.

The sum is not performing correctly. The first problem is when it falls in te default case, everything is 0, I've tried in the default with:

I have an app that uses requests to analyze and act on web page text. But it does not seem to work on this page that is likely built with angular: https://bio.tools/bowtie, in that the source HTML is different than the actual content. I am trying to collect the DOI that is referenced on the page (10.1186/gb-2009-10-3-r25), but when requests picks up the HTML source the DOI is not there.

I've heard that Google is able to parse pages that are generated using javascript. How do they do it? Any tips on viewing the DOI information with python?

Given a odd positive integer h, greater than or equal to 5, create a bowtie pattern with h rows and 2h columns.

I know this is a common error and I already checked other posts but it didn't resolved my issue. I would like to use the name of the database I use for SortMeRNA rule (rRNAdb=config["rRNA_database"]) the same way I use version=config["genome_version"]. But obviously, I can't.